Greenhouse gas (GHG) emissions from agroecosystems, particularly nitrous oxide (N₂O), are an increasing concern. To quantify N₂O emissions from agroecosystems, which occur as a result of nitrogen (N) cycling, a new physically-based routine was developed for the Soil and Water Assessment Tool (SWAT) model to predict N₂O flux during denitrification and an existing nitrification routine was modified to capture N₂O flux during this process. The new routines predict N₂O emissions by coupling the carbon (C) and N cycles with soil moisture/temperature and pH in SWAT. The model uses reduction functions to predict total denitrification (N₂+ N₂O) and partitions N₂ from N₂O using a ratio method. The modified SWAT nitrification routine likewise predicts N₂O emissions using reduction functions. The new denitrification routine and modified nitrification routine were tested using GRACEnet data at University Park, Pennsylvania, and West Lafayette, Indiana. Results showed strong correlations between plot measurements of N₂O flux and the model predictions for both test sites and suggest that N₂O emissions are particularly sensitive to soil pH and soil N, and moderately sensitive to soil temperature/moisture and total soil C levels.